Somber Leaf
by NoxraaTorgan
Summary: Set adrift into a different world, the banished King Sombra finds himself trapped within an infant Naruto Uzumaki the night he had the great Nine Tailed Foxed sealed within him. The dark king knows he has to be ready to retake the Crystal Empire, perhaps this child he is sealed in can prove useful. Collaboration with Mellra.
1. Chapter 1

Noxraa: Hi there, Noxraa Torgan here taking a moment out of _Vessel of Harmony_ to bring you another Naruto and My Little Pony crossover. This one is very different in premise however to _Vessel of Harmony._ That is because the story didn't come from me. So without further ado I present the writer behind the idea for _Somber Leaf_ , Mellra.

Mellra: Thanks Torgan. I read the MLP comic FIENDship is Magic that detailed King Sombra's origins and I couldn't help think; he is actually really similar to Naruto. Both are orphans, both were treated as outcasts, both had dark secrets about their origins, etc. The only difference is, Sombra gave in while Naruto didn't. That got me thinking, what would happen if these two were to meet? And then I thought about how some stories have characters from different series being sealed inside Naruto during the Kyuubi Attack and figured why not do the same with King Sombra?  
Around this time, I began reading _Vessel of Harmony_ and noticed how well Noxraa Torgan was able to do a Naruto/MLP crossover. So I decided to ask if they'd be interested in my idea and they said yes, so big shout out to Noxraa Torgan for listening to my madness! Here's hoping you all enjoy this story and all the fallout that will come from King Sombra being sealed in Naruto! Later!

Pain. Sheer agony beyond description.

That was the feeling King Sombra had when the Princesses of Night and Day had used their powers against him, turning him into shadows. The two so called benevolent rulers of Equestria had ripped him from his physical form; and they had the nerve to call him an evil king. Then, to add insult to injury, they had dared to banish him from the world of Equestria all together! This wasn't right. This isn't how it was supposed to be!

The dark king knew that the sisters would most likely defeat him when he heard of their coming thanks to the betrayal of Radiant Hope, but he had expected them to just send him back to the frozen wastelands where he originated from. Instead, he found himself being thrown out of the world he was destined to rule. Even now, after what felt like eons had past, King Sombra was trying to make sense of the world he was in.

In the world the overthrown king found himself in, ponies weren't the dominant species. Instead there were these strange creatures that looked like furless monkeys that he learned through observing them in his shadow form were called 'humans'. At first they seemed like weak, pathetic creatures. Even more pathetic than the Crystal Ponies, truth be told. However, Sombra soon learned that their appearance was deceiving.

While a large portion of their population were noncombatants, their soldiers displayed abilities that would probably even give an alicorn pause. The name chosen for these warriors was 'shinobi', or Warrior of the Shadows. Sombra, as a Shadow Pony, could see the irony of the situation, and also saw a possible opportunity with his banishment.

While he didn't expect to find himself banished into a completely different world, his curse on the Crystal Empire was still in effect. He could feel it, and when the Empire was to return in 1,000 years, so would Sombra. In the meantime, though, if he could find a way to harness the power of these shinobi, King Sombra saw this as a way to conquer Equestria with no contest! He would be able to defeat the alicorn princesses and their pathetic armies, regain his Crystal Pony slaves, free his umbrum brethren, and take over what is rightfully theirs with the power these shinobi possessed. The question was, how would he go about using their power to his advantage?

In his current state so far away from the magic of Equestria and the Crystal Empire, he was very close to powerless. His most prominent powers available at this time was his ability to travel through shadows and manipulating the minds of other beings. The downside to the latter is most shinobi have the mental discipline capable of resisting his manipulations, and he feared that pushing it would cause the shinobi to become aware of his presence. So he waited, watching, for the perfect opportunity to seize the power of the humans.

King Sombra was floating above the Village Hidden in the Leaves when he felt it. A crushing power, more so then he had ever felt before, practically saturated the area. Cautiously, the dark king went to investigate. What he saw caused the tyrant no small amount of surprise. Attacking the village was a GIANT fox with nine tails, and the shinobi fighting it seemed nearly powerless to even drive the beast back.

Immediately, Sombra saw an opportunity. If he could find some way to control the fox, or at the very least get it over to his side, he would be able to take over the Crystal Empire and Equestria in no time at all! Hay, he might even decide to expand his empire here in the human world if the Nine-Tails was as strong as he thought it was. However, there was still the same question as with the shinobi on how to take advantage of the fox. He didn't have long to ponder this though, as what appeared to be the village's leader arrived on the back of what seemed to be a giant toad to fight the beast. The battle was short but intense, ending with the blonde haired man using what looked to be a teleportation spell on the fox and transporting them out of the area.

The dark king nearly panicked as he frantically searched for where his future weapon had been taken, worried that the shinobi might destroy it before he could claim it. He didn't have far to look as he found the fox, along with the leader and a red haired woman and a newborn baby, in a clearing a distance from the main village. The man and the woman appeared to be pierced by one of the fox's enormous claws (Sombra idly noticed the fox seemed smaller than before and tied up in ethereal chains), and the two humans were talking to the baby in what must have been their final words. Sombra saw his chance, with the fox weakened by whatever ritual the humans had done to it, the umbrum could use his magic to take over the beast's mind. In his shadow form, the former ruler of the Crystal Empire flew towards the fox, his mouth forming a sharp toothed grin.

However, just as he was about to touch the fox to take over its mind, a bright light emitted from the man and engulfed both the fox and the dark unicorn, and all Sombra knew was darkness.

King Sombra groaned as he stood up. "Where…am I?" he wondered as he looked around his surroundings. He appeared to be in a mix between a dungeon and a sewer, with a pool of water formed at his hooves and pipes crisscrossing over the walls. It was then he noticed that he was trapped behind a large metal gate.

"What is the meaning of this?!" He roared in anger as his red horn glowed a dark purple color. Shooting off a concentrated blast of dark magic, the unicorn figured that his prison stay would be ended then and there. It was to his chagrin that the magic just seemed to harmlessly bounce against the bars before dissipating. Seeing that brute force wasn't the answer, Sombra took his shadow form and tried to simply float through the bars. The key word here being 'tried', as the moment he reached the bars he was thrown back by some sort of invisible barrier. Taking solid form once more, the king began to pace in front of the bars while trying to figure out what was going on.

"Well isn't this interesting. And here I thought I would have to wait for the brat to come visit me before I had any form of social interaction, yet here is a little pony being graced by my presence," a dark and sinister voice rumbled from across the room that was shrouded by darkness.

"Who's there? Show yourself!" Sombra demanded as he looked through the gloom.

"Hmph, quite the arrogant tone you're carrying little foal. We'll have to fix that now won't we?" The voice said in what the king believed to be a mocking tone. Just then, the darkness seemed to recede a little and Sombra could see across the room. On the other side was another cage that was easily ten times larger than his own, and held within the cage was none other than the Nine-Tailed Fox!

"You?! But, how did you…why are you…" Sombra began to stammer as he tried to comprehend why such a powerful creature was trapped in such a pathetic looking prison. Calming himself, the dark stallion then narrowed his shadowy green and red eyes at the Fox and said in his usual commanding air, "Where are we?"

The Nine-Tails gave a fanged smirk before answering. "First of all, you better check your tone with me in the future little colt, for even behind these bars I will find a way to show you how far beneath me you truly are. As for where we are, we were sealed inside that blonde infant those two humans were protecting. I can only assume you were stupid enough to get in the way as the sealing was taking place and now you are trapped in here with me until the day the brat dies."

Sombra's mind raced at the implications of the Fox's statement. He knew of sealing from his time observing the shinobi and he had seen them seal away objects like their tools and supplies in scrolls. This seal, however, must be absurdly powerful if it was able to imprison both the Fox and himself inside of a living being. The dark king decided that those were questions for later, as this beast had to know just who he was messing with.

"Watch your mouth you insolent cur! I am King Sombra, once and future ruler of the Crystal Empire in Equestria. I have vanquished princesses and placed countless ponies under my hoof! If you think I shall be intimidated by an oversized fox, then you are sorely mistaken!" Sombra barked as he gathered his dark magic around himself.

The Fox's only reaction was to quirk its brow. "A king, eh? That might be impressive if I have ever heard of a place called the Crystal Empire or Equestria, which I haven't."

Sombra sneered, "Of course you haven't, mongrel. It's in a completely different world from here. Through…extenuating circumstances, I was banished to this world until I regain my full power. Then, I will take my rightful place as not only king of the Crystal Empire, but ruler of the whole of Equestria!"

The Kyuubi gave a bemused look at this. "Sounds like quite the interesting tale, little pony," he then got into a more comfortable position on the floor and said, "Perhaps you can tell me more. After all, neither of us are going anywhere for a while. Then, perhaps, I might tell you a bit about my magnificent self."

While the Dark King didn't want to tell the arrogant fox anything, the pony remembered that he wanted the Fox's power on his side, so perhaps indulging the creature's curiosity may be the first steps in swaying the beast into helping him. So with that in mind, Sombra told the giant fox his story; how he was found in the artic wastes in the land of Equestria, his time in the orphanage, his friendship with Radiant Hope, his mysterious sickness during the Crystal Faire, the vision the Crystal Heart showed him, the discovery of his true nature, the defeat of Princess Amore, Radiant Hope's betrayal, the fight with the two Princesses, and finally his banishment to the Shinobi World after placing his curse upon the Crystal Empire.

Throughout it all, the Kyuubi listened without interrupting, his expression remaining blank. It was only after Sombra finished his tale that the Kyuubi spoke.

"And how do you plan on taking over Equestria while you are in this world, hmm? After all, now that you are sealed in this brat with me, you can't even look for a way to go back."

The unicorn snorted,

"I'm hardly as trapped as you may think. The royal fools that banished me beyond the realms of my world's reality must have believed that they would be rid of me forever. However, I made a failsafe within my curse. When the Crystal Empire shall return from its banishment from beyond the realms of time so shall I. As for being sealed in here…"

Sombra then pulsed his magic against the bars of his prison once more. He gave an evil grin as he felt that while the seal held strong against his might it had marginally weakened from his first assault.

"I can feel that this prison of ours, while made to store your 'chakra', is not made to contain my magic. While it is resisting me for now, I will only need a little more than a decade to break out of here." He smirked cruelly, "And then maybe I'll have this human we're sealed inside become an instrument for my wrath. Perhaps I'll have him wipe this village off the map under my influence, or maybe I'll take him with me to Equestria and have him destroy those meddling princesses!"

"Now that, my little pony, is a plan I can get behind," The Kyuubi remarked, getting King Sombra's attention. "Destroying those that wronged you is something that I can respect. In fact, I may even help you in your endeavors, as long as…" At this he trailed off as though contemplating something.

Barely daring to hope that it would be that simple to gain the monster's cooperation, Sombra asked, "As long as what?"

The Kyuubi smiled again, though Sombra noticed this smile was less malicious and more hopeful before he spoke again. "As long as you can ensure I will be released from this prison as well. I would also like to live in Equestria after helping you conquer it. A chance to live without having to deal with humans and not being sealed away again is too good of an opportunity to pass up!"

The dark unicorn king raised an eyebrow,

"You would leave behind the world of your birth just for the chance of not having to deal with humans?" At the question the Kyuubi let out a deep throated growl,

"Do you know what it is like to be seen only as a weapon? Since the humans discovered the method to control my kind we have been seen as nothing but assets to be thrown at our manipulator's enemies. I myself have not seen the outside world for more than an hour for the better part of a century. I have been sealed and resealed inside of human hosts without any consideration of our personal wishes." As the fox ranted on the anger and passion built behind his voice,

"The human race is vile and corrupt. They see me and my brethren as demons when it is them who are the true monsters! There has only been one human who has ever had, or who shall ever, be held in any respect in my eyes. I will forsake this world for another in a heartbeat and help you conquer your little kingdom if nothing more than to get away from a species that doesn't even bother to ask us if we have names!" The fox's final words echoed like summer thunder through the chamber and down unseen corridors. Eventually the demon's rant faded away and left the two occupants of the seal in silence.

Sombra considered the monstrous being's statement before replying,

"I will agree to this; but let us get one thing straight, I am the king and you will not interfere with my rule." Seeing the great fox nod in consent Sombra cackled, "Then we have an accord! Now all that remains is for the seal to weaken enough for me to influence this child. And," he glanced around the dimly lit sewer like prison, "Perhaps a change in décor is in order."

With that, the Umbrum stamped a hoof on the ground and the mindscape rumbled. Suddenly, the water covered floor cracked apart as dark and jagged crystals erupted forth. The water drained through the cracks and the walls of the seal began to peel away to reveal glimmering crystal gems embedded in the way. After several minutes of this, the room looked like less of a sewer and more of a diamond mine, the only things that remained unchanged was the bars on the two prisoners' cells.

The Kyuubi growled in a pleased tone. "Impressive."

King Sombra smirked,

"Quite. I figured the underground of the Crystal Empire is more appropriate a setting to be spending the next few years in. Now," At this his smoking green eyes seemed to glow maliciously,

"Let the games begin!"

Noxraa: And there you have it folks. The first instalment of _Somber Leaf._ If you liked what you read be sure to leave a comment in the little box below and tell us what you thought. If you really liked it share it with a friend or two. This is a shared story so updates may vary depending on who is writing the chapter; and of course life, because you know that happens. Until next time!


	2. Chapter 2

"He's been having nightmares again." Mai, caretaker for the village orphanage said to Hiruzen Sarutobi. The matron of the shelter was leading the aged leader of the Hidden Leaf up a flight of narrow stairs towards the loft of the orphanage.

"We've had to move him up here because his nightmares keep the other children up at night." She further explained. The elderly Hokage nodded in understanding

"Has he told you what his dreams are about?" Hiruzen asked. To this the matron shook her head,

"No, he hasn't told anyone what his dreams are about. Not even the other children."

"I highly doubt that he would confide in his peers. Considering," The Hokage let that statement trail off letting Mai know he was not pleased with her.

While the matron of the village orphanage was not cruel towards the charge given to her by the Hokage himself, she did nothing to dissuade the other children from repeating what they heard from the other adults around the village. Her inaction was just as bad as perpetuating the resentment demonstrated by the village.

It didn't help that Naruto behaved oddly himself. It seemed that he had a sort of bipolar disorder. There would be times he would be happy as can be then at the drop of a dime he would become angry, malicious even. This only fueled the fear of the village who were in the know about Naruto's jinchuriki status. They feared that the seal containing the Kyuubi was not as strong as it should be.

Of course Hiruzen had his best seal experts examine the last gift that the Fourth Hokage left for the village. There was no sign of defect or weakness in the array, as far as they could tell. He had consulted doctors to see if Naruto could be medicated and the village medics did agree to see if Naruto reacted to particular medicines. This was the Hokage's first visit since Naruto started on the medicines a few months ago, far too long in Hiruzen's opinion.

"Do you know if he is taking his medicine?"

"I try to administer it but it doesn't seem to help him. If anything the dreams are only getting worse."

This didn't bode well in Hiruzen's mind as they approached the top of the stairs. The loft was a long empty space that ran the length of the building. At the far end was a dirty window that filtered light through onto a single bed which sat under the window. Situated cross-legged on the bed, looking out on the world, was a blond haired boy. His whiskered face was expressionless as he looked out on the village. He didn't even turn around when the matron entered,

"Naruto, you have a visitor." The little boy turned around and an excited smile broke across Naruto's face. For the briefest of moments Hiruzen could have sworn that Naruto's eyes were red slits and a vibrant green color instead of his normal coloration. Hiruzen tried to convince himself otherwise because looking at them now they were the regular blue color

"Hey Gramps!" The Third Hokage crossed the loft and sat on the bed next to Naruto.

"Hello Naruto, how are you today?"

"Just looking out at everything, wishing someone would clean the window."

Hiruzen chuckled, though in his mind he was saddened when he noticed that Naruto was actually looking out at the playground where the other orphans were playing. Hoping to take the young boy's mind off of things while simultaneously trying to get to the bottom of Naruto's mysterious nightmares, he offered the boy a kind smile and said,

"Well Naruto, I was in the area and thought you'd might like to go and get some ramen with me while we catch up?"

"Ramen! Yes!" The youngster cheered enthusiastically before grabbing the elder man's hand and all but dragging him to the door while cheerfully rambling on, giving a quick goodbye to Mai in the process. The Third could only smile bemusedly at the child's antics.

Before long the two found themselves at the local ramen stand, Ichiraku's. The Hokage had one bowel in front of him while Naruto was already working on his second. Despite the child's enthusiasm, Hiruzen could pick up the telltale signs that Naruto hadn't been getting much sleep lately. His eyes had light shadows forming underneath them and his movements seemed slower than before. Not to mention that while Naruto had talked quite a bit, he was noticeably quieter than normal. To the untrained observer, Naruto would seem perfectly normal, but Hiruzen's long career as a shinobi allowed him to pick up on the small details on his surrogate grandson, and it worried him greatly.

"So, Naruto," the Third said in a casual manner, hoping to get the unpleasantness out of the way and get to the bottom of Naruto's mysterious nightmares. "how have things been for you lately? Are you having any trouble sleeping still?"

Naruto tensed for a second before he gave the Sarutobi a wide smile that was noticeably fake.

"Nope! Everything's been goin' fine Gramps. What about you? You ready to give me that hat yet?" he asked, obviously trying to steer the conversation away from its current course.

Hiruzen said in a calm tone, "No Naruto, I'm sure I have a good decade left in these bones of mine before I can retire." He decided to take a different tactic, "I noticed you are in a new room."

The boy nodded, "Yep! Ms. Mai said I can have it all to myself so I don't gotta hear the other kids' snoring."

"And how are you and the other children getting along? Making any new friends?" Hiruzen asked, already knowing the answer but hoping to be wrong for once.

The whisker marked boy's happy act faded somewhat as he stared at his ramen with a solemn expression. "No," he mumbled quietly, "They all say that they gotta stay away from me 'cause I'm a 'troublemaker' and that I'm 'weird'."

The Third sighed mentally, knowing that the children had most likely picked that up from other adults and cursed himself for being unable to do more for the boy besides making sure that his burden isn't openly discussed. No matter what laws are placed, people always find loopholes around them. Especially when it was about issues that caused people to become close minded on the matter.

Deciding to cheer the boy up a bit, Hiruzen affectionately ruffled Naruto's hair and told him,

"Don't worry about what others think of you, Naruto. People thought the First Hokage was weird too when he decided to form a shinobi village, but he persevered and was able to make the first and strongest village in the Elemental Nations. In fact, many great shinobi were thought of as either being weird or troublemakers in their time, yet they always showed the people how wrong they were. As long as you stay true to yourself and never falter from the path you are on, Naruto, I know that you will no doubt become a great shinobi in your own right."

Naruto gave a small but genuine smile at the sound advice and went back to his ramen. He was quiet for a couple of minutes and seemed to be mulling something over in his mind before turning back to the Third.

"Gramps," he said, "I…I actually could use your help. The nightmares still keep coming no matter what I try, and I'm getting so scared of them that I don't want to fall asleep! I haven't had a full night's sleep in nearly a week!"

Hiruzen frowned at that and turned to talk to the boy, hoping to find out what his nightmares were about and hopefully put his mind at ease. However, when he turned he noticed Naruto had actually fallen asleep right then and there, his head resting on the counter while snoring quietly. Gently, the Third picked him up after paying for their meals and carried him back to the orphanage, hoping that when the boy woke up he'd be more willing to talk to him about his nightmares. What the Third didn't realize is that, moments before falling asleep, Naruto's eyes turned a vibrant green color while his pupils became a scarlet hue.

Naruto walked happily to the Hokage's office before knocking on the door and letting himself in. "Hiyah Gramps! You ready to give me that hat yet?"

"Oh, it's you Naruto," came the cold reply that made Naruto wince at the tone, his eyes wide. The Third sat behind his desk like he normally would, but instead of the warm greeting smile was a look of pure disdain. It was a look Naruto had become all too familiar with in his young life as most of the villagers give him that look at one point or another, but not Gramps, never Gramps.

"So what are you doing here? Causing more trouble around the village no doubt to cause me to write more paperwork in order to clean up your mess. Or maybe you're here to blather on about how you're going to become Hokage like a broken record," he finished with a snort of derision.

"G-Gramps what d-do you mean?" Naruto stuttered as he tried unsuccessfully to hold back his tears as the one person he could always count on to be there was belittling him like so many others.

Hiruzen gave another snort as he got up from his chair and began to pace around Naruto with his hands behind his back.

"What I mean is that every day you're either in here because you caused some sort of problems for the hard working members of this village like the little troublemaker you are or you just want to bother me by saying how a talentless little nobody like yourself is going to reach the title of Hokage. Ha!" he laughed mockingly, "If you ever become Hokage, this village would be burned to the ground in less than a week! I'd much rather give my positon to someone who actually matters, not a sniveling, attention seeking, worthless little freak!"

Each word spoken to Naruto was like someone stabbed him with a kunai, twisted it, then pulled it out before stabbing him again. The blonde was openly crying now as his world seemed to crumble around him, dark shadows surrounding him at all sides.

The Third seemed to notice the boy's tears and said mercilessly, "Oh kami, are you crying now? I don't have time to deal with brats like you. Get out and stay out you failure!" he finished by picking the small child up by the collar of his shirt and throwing him out of the office with no mercy. Naruto landed on his bottom but the physical pain seemed nonexistent next to the emotional pain he was experiencing.

"G-Gramps…why?" he sobbed.

"Hey, look at the freak!" one of the passing villagers shouted as he pointed at the blonde and began to laugh. Soon, a crowd of people began to form and joined in on the jeering and laughing at the distraught child.

"What a loser!"

"Who would want a weirdo like that around?!"

"Moron!"

"Freak!"

"Monster!"

Naruto was so emotionally hurt that he didn't even notice that the shadows of a nearby building seemed to solidify into an equine shape. Green and red smoking eyes glittered maliciously from the shadows and a sharp toothed grin formed.

"Almost ready," a dark voice whispered eagerly as the owner of the voice stared at the crying blonde.

"No…stop…leave me alone," Naruto whimpered as he curled into a fetal position in an attempt to shield himself from the verbal onslaught. However, the laughter and catcalls continued and Naruto's pain started to turn into a mixture of emotions. Chief among them were grief, and rage. Naruto's eyes became the same color as the shadow figure's as a dark purple aura started to form around him.

"I said…STOP!" Naruto roared as the aura exploded around him, causing his surroundings to fade into blackness.

The Third was about to leave the orphanage when he felt it. After carrying a sleeping Naruto back to his room and putting him to bed, the man had a small talk with Mai asking her to inform him when Naruto woke up. He had just headed for the door when a pulse of power seemed to wash over him and the surrounding area, making the hairs on the back of his neck stand on end.

'What on earth?!' He thought as he had never felt an energy like this one before. It wasn't chakra, of that Hiruzen was confident in, but something else altogether. It was then he noticed the direction the feeling was coming from.

"Naruto!" He called frantically as he used all his speed from years of training to quickly go to his surrogate grandson's room.

What he saw upon opening the door shocked him, and considering the man had seen much during his shinobi career it spoke volumes of the magnitude of the situation. Naruto was now sitting up in his bed, obviously awake, and was crying into his hands. What was surprising though was that surrounding the boy was what looked like a jewelry store had exploded. Dark crystals, nearly obsidian in color and jagged like tree branches, surrounded the boy and covered the entire loft. They even crept up the walls and grew on the ceiling like stalactites. Hiruzen could only blink at the scene in surprise.

'I've heard of the Crystal Release Bloodline, but it's supposedly extremely rare. To see it manifest in Naruto in such a way…not to mention that energy I felt undoubtedly was what created the crystals, yet it felt like no chakra I have ever experienced. Could it be caused by the Fox?' Shaking those thoughts from his mind, the Sarutobi needed to check and make sure if Naruto was alright. Especially considering the fact that the blonde hadn't cried since he was a baby, so seeing him so openly weeping now was disheartening.

Carefully walking over the crystals and taking care not to get cut by the sharp edges, Hiruzen made his way over to the whiskered boy. Once he reached him, Hiruzen gently placed his arms around Naruto in a comforting embrace. The jinchuriki stiffened at the contact but quickly threw his arms around the man's waist as far as his small arms allowed and sobbed into the elder man's robes. Naruto was saying something, but due to his crying state, the fact he was talking into his robes, and that the boy was talking a mile a minute made it all but impossible to understand him.

"It's alright Naruto. It was just a nightmare. It cannot hurt you, not now or ever."

"It was so real. It was so real. It was so real." Naruto repeated and repeated into the old man's robes.

The two of them stayed like that for a good twenty minutes while Hiruzen did his best to calm the hysteric boy down. Eventually the orphaned boy fell asleep in the Hokage's arms. The aged leader allowed a sad smile to creep across his face,

'How long has it been since I've been able to do this for a child? Not since Asuma I think.' Hiruzen thought to himself.

The sound of slow footsteps came from the stairs outside the loft. Mia poked her head in through the door and was immediately taken aback by the forest of black crystal,

"Lord Hokage… What happened here?" She asked quietly as she could, trying not to wake the sleeping child.

"It would seem that Naruto is in possession of a rare bloodline limit. Though how he got it I am not sure. His nightmares probably triggered an instinctual defense."

Gingerly Mai touched one of the crystals that jutted out of the wall and jerked back her hand. She looked down at the finger that had barely pressed against the obsidian like crystals and watched blood trickle from an almost unseen cut in her flesh. Shaking her head, Mai looked back at the aged Hokage,

"I'm sorry sir, but he cannot stay here any longer. This ability he has is a danger to the other children. I'm sorry."

Ire mixed with understanding distilled on Hiruzen at Mai's words. He understood that as long as Naruto remained untrained in the ninja arts the boy was a threat to those around him. Especially if the crystal release was tied to the young boy's emotional state. With a nod Hiruzen agreed,

"I'll have him moved to an apartment elsewhere in the Village. I will be sending a team in to collect all of this." He said gesturing to the creeping crystals. That was when he noticed it. The light coming through the window, catching the crystals just right, made them all sparkle. There was a moment of calm as the two adults watched the glittering crystals.

"You know, in a certain light it's kind of beautiful." Mai commented.

"Even in tragedy there is a degree of beauty." Hiruzen commented.

Within the recesses of the seal King Sombra was smiling. It had taken him years to do it, but now the boy could handle the power of Equestrian magic flowing through him.

"That was very cruel of you, plaguing the whelp's mind with nightmares like that." Sombra's cellmate the Kyuubi commented, not actually caring for the wellbeing of their host.

"It was necessary for our plan. He had the power in him, he just needed… that little extra push." Sombra said with a wicked smile.

"No doubt the old monkey will be taking a greater interest in the brat's abilities. May even give him some personal trainers to help him learn to control his new 'blood line.'"

"Then we too must become more aware of what is going on out there." The horn atop the dark king lit up with his evil aura. Sombra charged a shot of his magic at the floor of the seal. The two prisoners watched as the crystals coving the chamber morphed into a kind of crystal archway large enough for an Ursa of Equestria to pass through unabated.

Sombra charged another spell and fired it into the archway. Colors started to fill the space within the arch until the image of Hiruzen Sarutobi carrying a sleeping Naruto Uzumaki through the darkening streets of Konohagakure.

"Now we shall be able to keep a closer eye on our _land lord_." Sombra said with an evil chuckle at the phrase.

"I will leave you to work your magic then." The fox said as it lay down its head and fell asleep. With a malicious smile Sombra looked on at the scene before him.

"Oh trust me, I will."

 _You must awake!_

Naruto's eyes were forced open into the fading hours of the day.

 _Look around, you are in new territory._

Following the direction of his inner voice Naruto looked around and indeed saw that he was no longer in the loft room of the orphanage. It was a sparsely furnished bedroom with a stand with some complicated machinery, which Naruto recognized well enough as hospital equipment, with a door leading out into a hall. Felling somewhat refreshed Naruto was about to get out of bed but the voice came again.

 _No, close your eyes and lay back down. There is much to be learned._

Not knowing why, Naruto listened to the voice and pretended to be asleep again. That was when he heard it voices from the hall,

"Are you sure you want to put him up there? I mean by all rights it is his but do we want him to know just how much weight his name could carry?" It was a voice unknown to Naruto, but the next voice he knew right away,

"There isn't much of a choice. Anywhere else in the village he could prove to be a danger if this new power of his is tied to his emotions. There he is not only safe but he is finally a part of the Uzumaki legacy."

'I am part of a legacy? I thought I was just an orphan.'

 _This is something to investigate at a later date. Prepare yourself, he is going to enter the room, pretend you know nothing._ The voice came again.

While Naruto had been warned that hearing voices was a bad thing this voice had not steered him wrong. He did learn a valuable piece of information. The boy thought that maybe he should listen to this voice some more.

The footsteps got closer to him and soon they were in his room. A gentle nudging and a familiar grandfatherly voice,

"Naruto, can you wake up?"

 _Go ahead and rise._

Trying his best to act like he waking up Naruto stirred and slowly sat up, rubbing sleep from his eyes,

"Gramps? Where are we? What happened?"

"Naruto, I'm afraid that Mai had to evict you from the orphanage. It's not that she didn't love you," Hiruzen quickly interceded, "It's just that your new ability could be a problem to others. Do you remember what happened in the orphanage?" Without waiting for an answer Hiruzen produced a shard of black crystal, "You had a nightmare and in your terror you unlocked a special ability. You covered your room in these black crystals."

Naruto took a moment to examine the glittering black shard,

"I made this?"

"Yes Naruto. It seems very similar to the Crystal Style, that is a technique that very few can utilize."

"How come I can use it then?" the six-year-old asked curiously.

Hiruzen pondered this for a second to find the right words a child who had yet to even enter the academy understand.

"You see, Naruto," He began slowly to make sure he didn't lose the boy's attention, "Sometimes, there are abilities that run in families which are called Bloodline Limits. These abilities are very rare and usually the only ones who can use those abilities come from that family. However," he stated, cutting off Naruto after seeing the eager look in the boy's eyes, already knowing what he would ask, "there are times when the ability skips several generations and can also be a result of a mix between a mother and father's Bloodline, creating something unique. The Wood Style that the First Hokage is a good example of this, as it was unique only to him. His brother, the Second Hokage, didn't have the Bloodline, although he was very talented in Water Style jutsu. I believe this is what happened with you Naruto, because as far as I am aware, no one in the Leaf has ever held the Crystal Release."

Naruto sighed and looked down, knowing he was probably not going to get any further clues to the identity of his parents today. He knew now that the Third was aware of their identities, but the old man most likely had his reasons for not telling him. The blonde's slightly bipolar nature came into play after a few minutes of sulking as he then brightened up.

"Well, at least I got a super cool new ability now!" He cheered, causing a chuckle from Hiruzen.

"That you do. That is another thing I wished to discuss with you, actually," Seeing he had the whiskered boy's attention, he continued, "Since your ability is largely an unknown and due to you no longer living in the orphanage, I was able to pull a few strings to get you set up in a new home that has plenty of space for you to practice your new abilities with. I've even arranged for a few shinobi to come by and oversee your training while instructing you as well."

Hiruzen was nearly knocked off the bed by the yellow missile named Naruto. The newly realized Crystal Release user jabbered on a mile a minute. "Thank you so much Gramps! This is the best gift ever! Just you wait, I'm gonna master this crystal stuff in no time and be ready to take your hat before you even know it!"

Hiruzen laughed as he gently ruffled the young Uzumaki's hair. "Of that I have no doubt, Naruto. This new ability of yours is quite the blessing in disguise, eh? Not only will it help you become a truly splendid shinobi, but it is actually that which allowed me to set you up with trainers and your new location. Normally for newly emancipated orphans, they are given an apartment along with a monthly stipend, but since there are loopholes in the laws of Konoha for newly awakened bloodline users, I was able to tweak it more for you."

"So where is this place, Gramps?" Naruto asked as he stared up at his grandfather figure questioningly.

"I'll take you to it after I get you discharged from the hospital," Hiruzen assured the blonde as he got up to go check the boy out with the hospital staff. It surprised the boy when he found out he was in the hospital, but then again the room was boring enough for it.

Fortunately, his stay was brief as he was discharged as soon as the Third came back. The two walked some distance away from the hospital to a part of the village Naruto had never explored before. The buildings became more spaced and there were more trees in the area. Soon the two arrived in front of what appeared to be an old clan compound. It wasn't the largest, only around half the size of the Uchiha District, but it was still quite spacious. There were signs that the place hadn't been lived in for quite some time as all the buildings inside the gate were dark and quiet, but it was obviously taken care of to an extent as the yards were neatly trimmed and the paint hadn't faded from the houses, indicating someone had been maintenance the place. In the center of it all was a large temple that was nearly ten stories tall. What really got the boy's attention though was the red spiral he saw on many Jonin and Chunin were one of the main decorations here.

"What is this place?" Naruto asked in wonder.

"This, Naruto, is the Uzumaki compound," Hiruzen explained.

The boy whipped around and stared at the old man in wide eyed shock.

"W-wait, Gramps, you mean-?"

Hiruzen knelt down to the boy's level and said in a serious tone,

"Naruto, I cannot tell you everything because you're too young to understand yet, but I will tell you what I can. Do you understand?"

Naruto excitedly nodded his head, more than eager to hear about his possible identity. The Third began in a lecturing tone of voice,

"The Uzumaki Clan was a branched off part of the Senju Clan. The two had a close relationship, and after the villages were built they still had a strong connection despite the fact that a majority of the Uzumaki continued to live on the island village of Whirlpool. In fact, this compound was built close to the Senju compound for that very reason. The compound was built for any Uzumaki who wished to live closer to their cousins as a sign of friendship."

"What happened to them Gramps? Why haven't I heard about them?" Naruto asked, partially fearing the answer.

A sad look overcame Hiruzen's face.

"Because of their close relationship to Konoha, Whirlpool was one of the first targets during the Second Shinobi War. The attack was so fierce and brutal that there were only a few survivors,

"What happened to them?" Naruto asked with a slight glimmer of hope. The reply was a sad shake of the head,

"Those that survived the massacre were scattered to the winds. The few Uzumaki that were in Konoha at the time died shortly after from various circumstances such as the war and old age. You yourself are a descendant of the Uzumaki Clan from your mother's side, but she died during the Kyuubi Attack."

Seeing Naruto's crestfallen look, Hiruzen gently placed a hand on Naruto's shoulder.

"I'm sorry for not telling you this sooner, Naruto, but I did have my reasons. You see, your mother was special even among the Uzumaki Clan. As such, she had many enemies both in and outside the village. She even had a kidnapping attempt on her by the Hidden Cloud when she was a Genin. I had hoped that by keeping your heritage secret, even from you, for a while would both give you time to prepare to face any threats and also hopefully give those who would seek out the remaining Uzumaki a false sense of security. However, your bloodline awakening has pushed you knowing forward, as this is the best place for you to practice your new bloodline. I hope you can forgive me for leaving you in the dark about this Naruto, I only did it in order to protect you," He finished somberly.

Naruto sniffled a bit before wiping his eyes with his sleeve and looking up to his grandfather figure. While it did hurt that the knowledge of his family was kept secret from him, Naruto did understand that it was done with his best interest in mind as Gramps never tried to hurt him, unlike that nightmare version that awoke his bloodline. As Naruto hugged the old man once again though, the voice from before did give him pause.

 _He's still hiding something._

The boy decided to ignore it for now though as he followed his Gramps to get the tour of his new home. Just like with his clan, Naruto was certain all things would be revealed to him in time. For now, he had a new home to settle in.

In a shadowy room, a man who had most of his head wrapped in bandages and an arm missing stared impassively at the figure kneeling before him.

"And you are sure this information is accurate?" Danzo Shimura questioned.

"Yes Lord Danzo," the kneeling Root operative answered in an emotionless voice. "According to the orphanage staff, Naruto Uzumaki was moved out of the orphanage into the old Uzumaki Compound after experiencing what appears to be the awakening of a new bloodline."

Danzo hummed for a moment before turning to his subordinate. "Very well. Continue to monitor the situation and report to me on any new developments."

The masked ninja nodded wordlessly before vanishing in a whirlwind of leaves. Danzo meanwhile turned his attention to the only window in the room that showed Konoha at nighttime.

So, the Kyuubi jinchuriki had awakened a bloodline previously unseen in the Leaf and was now learning more about his heritage on his mother's side. The old warhawk pondered how he could use this for the village's benefit. After all, everything he did was for the village, even if he had to do it from the shadows.

A/N

Noxraa: Alright folks there you have it, chapter two of Somber Leaf. It took us a while but I hope the length of the chapter makes up for our lack of speed in getting this out to you all.

Now some of you in the comment section raised concern if this fiction would contain an evil Naruto. To dismiss your fears Naruto will not be EVIL, there maybe a few times when his normal personality will dim but he will not rain dark crystals and destruction upon those who have wronged him in the past. So I hope that puts your minds at ease

Anyways, Mellra and I hope you have enjoyed this chapter. Please leave a comment and share it with your friends


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